How to extract the Cancer Cell Fraction for copy number lesions (eg. 8q23.3) from ABSOLUTE output?

[sunand...@gmail.com]

To provide more information: Absolute ran successfully on segmentation and maf files for each sample in my study. The .RData files have been generated on each sample. Here is the summary of one of the samples

> summary(seg.dat)
                Length Class      Mode    
segtab           8     data.frame list    
error_model      0     -none-     list    
primary.disease  1     -none-     character
group            1     -none-     character
platform         1     -none-     character
sample.name      1     -none-     character
array.name       1     -none-     character
maf.fn           1     -none-     character
obs.scna         8     -none-     list    
mut.cn.dat       8     data.frame list    
mode.res        14     -none-     list    
version          1     -none-     numeric  

Where can i find the Cancer cell fraction (CCF) for a particular lesion (say 8q23.3) in this seg.dat list generated as Absolute output?

[Ted Liefeld]

Hi

unfortunately we do not have any experience with Absolute in the GenePattern team.  I asked a colleague at the Broad Institute and he suggested looking into the segtab dataframe from your output to see if there was anything in there.  Sorry we can't offer more help

Ted